(1) Background: The link between diabetes and hypertension is mutual and reciprocal, increasing the risks for the development of atrial fibrillation (AF). The main objective was to develop a prediction model for AF in a population with both diabetes and hypertension at five years of follow-up. (2) Methods: A multicenter and community-based cohort study was undertaken of 8237 hypertensive diabetic patients without AF between 1 January 2103 and 31 December 2017. Multivariate Cox proportional-hazards regression models were used to identify predictors AF and to stratify risk scores by quartiles. (3) Results: AF incidence was 10.5/1000 people/years (95% confidence interval (CI) 9.5–11.5), higher in men. The independent prognostic factors identified: age (hazard ratio (HR) 1.07 95% CI 1.05–1.09, p < 0.001), weight (HR 1.03 95% CI 1.02–1.04, p < 0.001), CHA2DS2VASc score (HR 1.57 95% CI 1.16–2.13, p = 0.003) and female gender (HR 0.55 95% CI 0.37–0.82, p = 0.004). Q4 (highest-risk group for AF) had the highest AF incidence, stroke and mortality, and the smallest number needed to screen to detect one case of AF. (4) Conclusions: Risk-based screening for AF should be used in high cardiovascular risk patients as the hypertensive diabetics, for treatment of modifiable cardiovascular risk, and monitoring AF detection.